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  1. Clostridium difficile is an opportunistic human intestinal pathogen, and C. difficile infection (CDI) is one of the main causes of antibiotic-induced diarrhea and colitis. One successful approach to combat CDI, p...

    Authors: Vijay Shankar, Matthew J Hamilton, Alexander Khoruts, Amanda Kilburn, Tatsuya Unno, Oleg Paliy and Michael J Sadowsky

    Citation: Microbiome 2014 2:13

    Content type: Research

    Published on:

  2. To augment capacity-building for microbiome and probiotic research in Africa, a workshop was held in Nairobi, Kenya, at which researchers discussed human, animal, insect, and agricultural microbiome and probio...

    Authors: Gregor Reid, Nicholas Nduti, Wilbert Sybesma, Remco Kort, Tobias R Kollmann, Rod Adam, Hamadi Boga, Eric M Brown, Alexandra Einerhand, Hani El-Nezami, Gregory B Gloor, Irene I Kavere, Johanna Lindahl, Amee Manges, Wondu Mamo, Rocio Martin…

    Citation: Microbiome 2014 2:12

    Content type: Meeting Report

    Published on:

  3. Authors: Roberto Romero, Sonia S Hassan, Pawel Gajer, Adi L Tarca, Douglas W Fadrosh, Lorraine Nikita, Marisa Galuppi, Ronald F Lamont, Piya Chaemsaithong, Jezid Miranda, Tinnakorn Chaiworapongsa and Jacques Ravel

    Citation: Microbiome 2014 2:10

    Content type: Erratum

    Published on:

    The original article was published in Microbiome 2014 2:4

  4. Culture-independent molecular surveys targeting conserved marker genes, most notably 16S rRNA, to assess microbial diversity remain semi-quantitative due to variations in the number of gene copies between spec...

    Authors: Florent E Angly, Paul G Dennis, Adam Skarshewski, Inka Vanwonterghem, Philip Hugenholtz and Gene W Tyson

    Citation: Microbiome 2014 2:11

    Content type: Methodology

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  7. Humans can spend the majority of their time indoors, but little is known about the interactions between the human and built-environment microbiomes or the forces that drive microbial community assembly in the ...

    Authors: James F Meadow, Adam E Altrichter, Steven W Kembel, Maxwell Moriyama, Timothy K O’Connor, Ann M Womack, G Z Brown, Jessica L Green and Brendan J M Bohannan

    Citation: Microbiome 2014 2:7

    Content type: Research

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  8. To take advantage of affordable high-throughput next-generation sequencing technologies to characterize microbial community composition often requires the development of improved methods to overcome technical ...

    Authors: Douglas W Fadrosh, Bing Ma, Pawel Gajer, Naomi Sengamalay, Sandra Ott, Rebecca M Brotman and Jacques Ravel

    Citation: Microbiome 2014 2:6

    Content type: Methodology

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  9. Mucosal biopsy is the most common sampling technique used to assess microbial communities associated with the intestinal mucosa. Biopsies disrupt the epithelium and can be associated with complications such as...

    Authors: Susan M Huse, Vincent B Young, Hilary G Morrison, Dionysios A Antonopoulos, John Kwon, Sushila Dalal, Rose Arrieta, Nathaniel A Hubert, Lici Shen, Joseph H Vineis, Jason C Koval, Mitchell L Sogin, Eugene B Chang and Laura E Raffals

    Citation: Microbiome 2014 2:5

    Content type: Research

    Published on:

  10. This study was undertaken to characterize the vaginal microbiota throughout normal human pregnancy using sequence-based techniques. We compared the vaginal microbial composition of non-pregnant patients with a...

    Authors: Roberto Romero, Sonia S Hassan, Pawel Gajer, Adi L Tarca, Douglas W Fadrosh, Lorraine Nikita, Marisa Galuppi, Ronald F Lamont, Piya Chaemsaithong, Jezid Miranda, Tinnakorn Chaiworapongsa and Jacques Ravel

    Citation: Microbiome 2014 2:4

    Content type: Research

    Published on:

    The Erratum to this article has been published in Microbiome 2014 2:10

  11. Shotgun metagenomics has become an important tool for investigating the ecology of microorganisms. Underlying these investigations is the assumption that metagenome sequence data accurately estimates the censu...

    Authors: Rachel Marine, Coleen McCarren, Vansay Vorrasane, Dan Nasko, Erin Crowgey, Shawn W Polson and K Eric Wommack

    Citation: Microbiome 2014 2:3

    Content type: Research

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  12. The source inoculum of gastrointestinal tract (GIT) microbes is largely influenced by delivery mode in full-term infants, but these influences may be decoupled in very low birth weight (VLBW, <1,500 g) neonate...

    Authors: Brandon Brooks, Brian A Firek, Christopher S Miller, Itai Sharon, Brian C Thomas, Robyn Baker, Michael J Morowitz and Jillian F Banfield

    Citation: Microbiome 2014 2:1

    Content type: Research

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  14. Psoriasis is a common chronic inflammatory disease of the skin. We sought to characterize and compare the cutaneous microbiota of psoriatic lesions (lesion group), unaffected contralateral skin from psoriatic ...

    Authors: Alexander V Alekseyenko, Guillermo I Perez-Perez, Aieska De Souza, Bruce Strober, Zhan Gao, Monika Bihan, Kelvin Li, Barbara A Methé and Martin J Blaser

    Citation: Microbiome 2013 1:31

    Content type: Research

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  15. The premature infant gut has low individual but high inter-individual microbial diversity compared with adults. Based on prior 16S rRNA gene surveys, many species from this environment are expected to be simil...

    Authors: Christopher T Brown, Itai Sharon, Brian C Thomas, Cindy J Castelle, Michael J Morowitz and Jillian F Banfield

    Citation: Microbiome 2013 1:30

    Content type: Research

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  16. Bacterial vaginosis (BV) is a common gynecologic diagnosis characterized by dysbiosis of the vaginal microbiota. It is often accompanied by vaginal symptoms such as odor and discharge, but can be asymptomatic....

    Authors: Jacques Ravel, Rebecca M Brotman, Pawel Gajer, Bing Ma, Melissa Nandy, Douglas W Fadrosh, Joyce Sakamoto, Sara SK Koenig, Li Fu, Xia Zhou, Roxana J Hickey, Jane R Schwebke and Larry J Forney

    Citation: Microbiome 2013 1:29

    Content type: Microbiome Announcement

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  17. The Atacama Desert is one of the driest deserts in the world and its soil, with extremely low moisture, organic carbon content, and oxidizing conditions, is considered to be at the dry limit for life.

    Authors: Alexander Crits-Christoph, Courtney K Robinson, Tyler Barnum, W Florian Fricke, Alfonso F Davila, Bruno Jedynak, Christopher P McKay and Jocelyne DiRuggiero

    Citation: Microbiome 2013 1:28

    Content type: Research

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  18. Cystic fibrosis (CF) is caused by inherited mutations in the cystic fibrosis transmembrane conductance regulator gene and results in a lung environment that is highly conducive to polymicrobial infection. Over...

    Authors: Katherine E Price, Thomas H Hampton, Alex H Gifford, Emily L Dolben, Deborah A Hogan, Hilary G Morrison, Mitchell L Sogin and George A O’Toole

    Citation: Microbiome 2013 1:27

    Content type: Research

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  19. Regardless of infection route, the intestine is the primary site for HIV-1 infection establishment and results in significant mucosal CD4+ T lymphocyte depletion, induces an inflammatory state that propagates ...

    Authors: Ian H McHardy, Xiaoxiao Li, Maomeng Tong, Paul Ruegger, Jonathan Jacobs, James Borneman, Peter Anton and Jonathan Braun

    Citation: Microbiome 2013 1:26

    Content type: Research

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  20. Our knowledge of microbial diversity in the human oral cavity has vastly expanded during the last two decades of research. However, much of what is known about the behavior of oral species to date derives from...

    Authors: Anna Edlund, Youngik Yang, Adam P Hall, Lihong Guo, Renate Lux, Xuesong He, Karen E Nelson, Kenneth H Nealson, Shibu Yooseph, Wenyuan Shi and Jeffrey S McLean

    Citation: Microbiome 2013 1:25

    Content type: Methodology

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  22. Formation of operational taxonomic units (OTU) is a common approach to data aggregation in microbial ecology studies based on amplification and sequencing of individual gene targets. The de novo assembly of OTU s...

    Authors: Matthew G Links, Bonnie Chaban, Sean M Hemmingsen, Kevin Muirhead and Janet E Hill

    Citation: Microbiome 2013 1:23

    Content type: Methodology

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  23. Sediments are massive reservoirs of carbon compounds and host a large fraction of microbial life. Microorganisms within terrestrial aquifer sediments control buried organic carbon turnover, degrade organic con...

    Authors: Laura A Hug, Cindy J Castelle, Kelly C Wrighton, Brian C Thomas, Itai Sharon, Kyle R Frischkorn, Kenneth H Williams, Susannah G Tringe and Jillian F Banfield

    Citation: Microbiome 2013 1:22

    Content type: Research

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  24. Soil is among the most diverse and complex environments in the world. Soil microorganisms play an essential role in biogeochemical cycles and affect plant growth and crop production. However, our knowledge of ...

    Authors: Nicolás Rascovan, Belén Carbonetto, Santiago Revale, Marina D Reinert, Roberto Alvarez, Alicia M Godeas, Roxana Colombo, Mario Aguilar, María Victoria Novas, Leopoldo Iannone, Alicia M Zelada, Alejandro Pardo, Gustavo Schrauf, Alejandro Mentaberry and Martín P Vazquez

    Citation: Microbiome 2013 1:21

    Content type: Microbiome Announcement

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  25. Preterm infants represent a unique patient population that is born functionally immature and must accomplish development under the influence of a hospital environment. Neonatal necrotizing enterocolitis (NEC) ...

    Authors: Erika C Claud, Kevin P Keegan, Jennifer M Brulc, Lei Lu, Daniela Bartels, Elizabeth Glass, Eugene B Chang, Folker Meyer and Dionysios A Antonopoulos

    Citation: Microbiome 2013 1:20

    Content type: Research

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  26. The lung microbiome of healthy individuals frequently harbors oral organisms. Despite evidence that microaspiration is commonly associated with smoking-related lung diseases, the effects of lung microbiome enr...

    Authors: Leopoldo N Segal, Alexander V Alekseyenko, Jose C Clemente, Rohan Kulkarni, Benjamin Wu, Hao Chen, Kenneth I Berger, Roberta M Goldring, William N Rom, Martin J Blaser and Michael D Weiden

    Citation: Microbiome 2013 1:19

    Content type: Research

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    The Erratum to this article has been published in Microbiome 2014 2:21

  27. Antimicrobial use is thought to suppress the intestinal microbiota, thereby impairing colonization resistance and allowing Clostridium difficile to infect the gut. Additional risk factors such as proton-pump inhi...

    Authors: Caroline Vincent, David A Stephens, Vivian G Loo, Thaddeus J Edens, Marcel A Behr, Ken Dewar and Amee R Manges

    Citation: Microbiome 2013 1:18

    Content type: Research

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  28. Consistent compositional shifts in the gut microbiota are observed in IBD and other chronic intestinal disorders and may contribute to pathogenesis. The identities of microbial biomolecular mechanisms and meta...

    Authors: Ian H McHardy, Maryam Goudarzi, Maomeng Tong, Paul M Ruegger, Emma Schwager, John R Weger, Thomas G Graeber, Justin L Sonnenburg, Steve Horvath, Curtis Huttenhower, Dermot PB McGovern, Albert J Fornace Jr., James Borneman and Jonathan Braun

    Citation: Microbiome 2013 1:17

    Content type: Research

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  29. Numerous cancers have been linked to microorganisms. Given that colorectal cancer is a leading cause of cancer deaths and the colon is continuously exposed to a high diversity of microbes, the relationship bet...

    Authors: René L Warren, Douglas J Freeman, Stephen Pleasance, Peter Watson, Richard A Moore, Kyla Cochrane, Emma Allen-Vercoe and Robert A Holt

    Citation: Microbiome 2013 1:16

    Content type: Research

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  30. The aberrant inflammation that is the hallmark of the inflammatory bowel diseases (IBD) is associated with several factors, including changes in the intestinal microbiota. Here, we confirmed that an intestinal...

    Authors: Nabeetha A Nagalingam, Courtney J Robinson, Ingrid L Bergin, Kathryn A Eaton, Gary B Huffnagle and Vincent B Young

    Citation: Microbiome 2013 1:15

    Content type: Research

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  32. Necrotizing enterocolitis (NEC) is a devastating intestinal disease that afflicts 10% of extremely preterm infants. The contribution of early intestinal colonization to NEC onset is not understood, and predict...

    Authors: Ardythe L Morrow, Anne J Lagomarcino, Kurt R Schibler, Diana H Taft, Zhuoteng Yu, Bo Wang, Mekibib Altaye, Michael Wagner, Dirk Gevers, Doyle V Ward, Michael A Kennedy, Curtis Huttenhower and David S Newburg

    Citation: Microbiome 2013 1:13

    Content type: Research

    Published on:

  33. Bacterial vaginosis (BV), the most common vaginal condition of reproductive-aged women, is associated with a highly diverse and heterogeneous microbiota. Here we present a proof-of-principle analysis to uncove...

    Authors: Jean M Macklaim, Andrew D Fernandes, Julia M Di Bella, Jo-Anne Hammond, Gregor Reid and Gregory B Gloor

    Citation: Microbiome 2013 1:12

    Content type: Research

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  34. Recent advances in next-generation DNA sequencing enable rapid high-throughput quantitation of microbial community composition in human samples, opening up a new field of microbiomics. One of the promises of t...

    Authors: Alexander Statnikov, Mikael Henaff, Varun Narendra, Kranti Konganti, Zhiguo Li, Liying Yang, Zhiheng Pei, Martin J Blaser, Constantin F Aliferis and Alexander V Alekseyenko

    Citation: Microbiome 2013 1:11

    Content type: Research

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  36. The indigenous gut microbiota are thought to play a crucial role in the development and maintenance of the abnormal inflammatory responses that are the hallmark of inflammatory bowel disease. Direct tests of t...

    Authors: Vincent B Young, Laura H Raffals, Susan M Huse, Marius Vital, Dongjuan Dai, Patrick D Schloss, Jennifer M Brulc, Dionysios A Antonopoulos, Rose L Arrieta, John H Kwon, K Gautham Reddy, Nathaniel A Hubert, Sharon L Grim, Joseph H Vineis, Sushila Dalal, Hilary G Morrison…

    Citation: Microbiome 2013 1:9

    Content type: Research

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  37. Butyrate, which is produced by the human microbiome, is essential for awell-functioning colon. Bacteria that produce butyrate are phylogeneticallydiverse, which hinders their accurate detection based on conven...

    Authors: Marius Vital, Christopher R Penton, Qiong Wang, Vincent B Young, Dion A Antonopoulos, Mitchell L Sogin, Hilary G Morrison, Laura Raffals, Eugene B Chang, Gary B Huffnagle, Thomas M Schmidt, James R Cole and James M Tiedje

    Citation: Microbiome 2013 1:8

    Content type: Research

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  38. Murine norovirus (MNV) is the most common gastrointestinal pathogen of research mice and can alter research outcomes in biomedical mouse models of inflammatory bowel disease (IBD). Despite indications that an ...

    Authors: Adam M Nelson, Michael D Elftman, Amelia K Pinto, Megan Baldridge, Patrick Hooper, Justin Kuczynski, Joseph F Petrosino, Vincent B Young and Christiane E Wobus

    Citation: Microbiome 2013 1:7

    Content type: Research

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  39. Besides the development of comprehensive tools for high-throughput 16S ribosomal RNA amplicon sequence analysis, there exists a growing need for protocols emphasizing alternative phylogenetic markers such as t...

    Authors: James Robert White, Cynthia Maddox, Owen White, Samuel V Angiuoli and W Florian Fricke

    Citation: Microbiome 2013 1:6

    Content type: Methodology

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  40. Viruses are important drivers of ecosystem functions, yet little is known about the vast majority of viruses. Viral shotgun metagenomics enables the investigation of broad ecological questions in phage communi...

    Authors: Heather K Allen, John Bunge, James A Foster, Darrell O Bayles and Thaddeus B Stanton

    Citation: Microbiome 2013 1:5

    Content type: Research

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  41. The use of culture-independent nucleic acid techniques, such as ribosomal RNA gene cloning library analysis, has unveiled the tremendous microbial diversity that exists in natural environments. In sharp contra...

    Authors: Weimin Gao, Dena Navarroli, Jared Naimark, Weiwen Zhang, Shih-hui Chao and Deirdre R Meldrum

    Citation: Microbiome 2013 1:4

    Content type: Methodology

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  42. Fecal bacteriotherapy (‘stool transplant’) can be effective in treating recurrent Clostridium difficile infection, but concerns of donor infection transmission and patient acceptance limit its use. Here we descri...

    Authors: Elaine O Petrof, Gregory B Gloor, Stephen J Vanner, Scott J Weese, David Carter, Michelle C Daigneault, Eric M Brown, Kathleen Schroeter and Emma Allen-Vercoe

    Citation: Microbiome 2013 1:3

    Content type: Methodology

    Published on:

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